First version of if inverted repeat annotation tools

Former-commit-id: 9d13deae459b086f11ba4f0f82aac899b4ff0fd9
Former-commit-id: 74a7f07d3fb26f6ce12808b8fe2dc7f176181285

detectors/normalize/lib/lookforIR.lib.sh

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+source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
+
+SELECTIR="${PROG_DIR}/../../normalize/lib/selectIR.py"
+
+function lookForIR {
+
+	local QUERY="$1"
+	local MATCHES=$(basename ${QUERY})
+	      MATCHES="${MATCHES/.*/}.matches"
+	
+	local REPEATS="${MATCHES/.*/}.repseek"
+	
+	loginfo "Locating SSC and LSC by similarity..."
+		blastn -db ${SCDB} \
+		       -query ${QUERY} \
+		       -outfmt 6 \
+		       -max_target_seqs 10000 | \
+		  awk '($4 > 1000) && ($3>80) { \
+		             SAME=(($7 < $8) && ($9 < $10)) || (($7 > $8) && ($9 > $10)); \
+			 		 if ($7 < $8) \
+			 			{print substr($2,1,3),$7,$8,SAME}  \
+			 		 else \
+			 			{print substr($2,1,3),$8,$7,SAME}}' | \
+		  sort -nk 2 > ${MATCHES}
+	loginfo "Done"
+	  
+	loginfo "Looking for long inverted repeats..."
+		repseek -c -p 0.001 -i ${QUERY} 2>> /dev/null > ${REPEATS}
+		loginfo " --> $(wc -l ${REPEATS} | awk '{print $1}') repeats identified"
+	loginfo "Done"
+	
+	loginfo "Marking and selecting the best inverted repeat..."
+		local IR=( $(${SELECTIR} ${MATCHES} ${REPEATS}) )
+	loginfo "Done"
+	
+	loginfo " --> IR size : IRa = ${IR[5]} /  IRb = ${IR[7]}"
+	loginfo " --> IR Score: ${IR[8]}"
+	
+	let "deltaIR=${IR[5]} -  ${IR[7]}"
+	
+	if (( $deltaIR < -10 )) ||  (( $deltaIR > 10 )); then
+		logwarning "Differences between IR lengths ($deltaIR) is greater than 10"
+	fi
+	
+	
+	echo "${IR[@]}"
+}
+
+SCDB="${IR_DATA_DIR}/SC_RefDB"
+QUERY="${CALL_DIR}/$1"
+
+
+openLogFile "${QUERY/.*/}.log"